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<div class="title">diffusion_reaction_particles.h</div>  </div>
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<a href="diffusion__reaction__particles_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/* -------------------------------------------------------------------------*</span></div><div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">*                               SPHinXsys                                   *</span></div><div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">* --------------------------------------------------------------------------*</span></div><div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* SPHinXsys (pronunciation: s&#39;finksis) is an acronym from Smoothed Particle *</span></div><div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* Hydrodynamics for industrial compleX systems. It provides C++ APIs for    *</span></div><div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* physical accurate simulation and aims to model coupled industrial dynamic *</span></div><div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* systems including fluid, solid, multi-body dynamics and beyond with SPH   *</span></div><div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* (smoothed particle hydrodynamics), a meshless computational method using  *</span></div><div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">* particle discretization.                                                  *</span></div><div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">*                                                                           *</span></div><div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">* SPHinXsys is partially funded by German Research Foundation               *</span></div><div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">* (Deutsche Forschungsgemeinschaft) DFG HU1527/6-1, HU1527/10-1             *</span></div><div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">* and HU1527/12-1.                                                          *</span></div><div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">*                                                                           *</span></div><div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">* Portions copyright (c) 2017-2020 Technical University of Munich and       *</span></div><div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">* the authors&#39; affiliations.                                                *</span></div><div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">*                                                                           *</span></div><div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">* Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may   *</span></div><div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">* not use this file except in compliance with the License. You may obtain a *</span></div><div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">* copy of the License at http://www.apache.org/licenses/LICENSE-2.0.        *</span></div><div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">*                                                                           *</span></div><div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">* --------------------------------------------------------------------------*/</span></div><div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;</div><div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<span class="preprocessor">#include &quot;base_particles.h&quot;</span></div><div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="base__material_8h.html">base_material.h</a>&quot;</span></div><div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="base__body_8h.html">base_body.h</a>&quot;</span></div><div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor">#include &quot;diffusion_reaction.h&quot;</span></div><div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="solid__particles_8h.html">solid_particles.h</a>&quot;</span></div><div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="xml__engine_8h.html">xml_engine.h</a>&quot;</span></div><div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;fstream&gt;</span></div><div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;</div><div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="keyword">using namespace </span><a class="code" href="namespacestd.html">std</a>;</div><div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="keyword">namespace </span><a class="code" href="namespace_s_p_h.html">SPH</a> {</div><div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;</div><div class="line"><a name="l00049"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_data.html">   49</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a></div><div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;    {</div><div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>(<span class="keywordtype">size_t</span> number_of_species);</div><div class="line"><a name="l00054"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_data.html#a387eae85205f80dd35b898faee438ad5">   54</a></span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>() {};</div><div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;</div><div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;        <a class="code" href="class_std_vec_3_01_real_01_4.html">StdVec&lt;Real&gt;</a> species_n_;</div><div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_data.html#a225749466f115c22bae74deb18140ce7">   59</a></span>&#160;        <a class="code" href="class_std_vec_3_01_real_01_4.html">StdVec&lt;Real&gt;</a> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a225749466f115c22bae74deb18140ce7">species_s_</a>;</div><div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_data.html#a9c9c5fa76e83b20f66c7eb961dea9b76">   61</a></span>&#160;        <a class="code" href="class_std_vec_3_01_real_01_4.html">StdVec&lt;Real&gt;</a>  <a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html#a9c9c5fa76e83b20f66c7eb961dea9b76">dspecies_dt_</a>;</div><div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;    };</div><div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div><div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BaseParticlesType = BaseParticles, <span class="keyword">class</span> BaseMaterialType = BaseMaterial&gt;</div><div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles</a> : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a></div><div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    {</div><div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#af4fd7b9302042ace3975690235e3cf25">   73</a></span>&#160;        <span class="keywordtype">size_t</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#af4fd7b9302042ace3975690235e3cf25">number_of_species_</a>;</div><div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;        <a class="code" href="classmap_3_01string_00_01size__t_01_4.html">map&lt;string, size_t&gt;</a> species_indexes_map_;</div><div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#ace9886026ada5948e27c14a0ce827b2f">   77</a></span>&#160;        StdLargeVec&lt;DiffusionReactionData&gt; <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#ace9886026ada5948e27c14a0ce827b2f">diffusion_reaction_data_</a>;</div><div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;</div><div class="line"><a name="l00080"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#ab0a715f35dc6105562f81bac0eb2852b">   80</a></span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#ab0a715f35dc6105562f81bac0eb2852b">DiffusionReactionParticles</a>(<a class="code" href="class_s_p_h_1_1_s_p_h_body.html">SPHBody</a>* body, </div><div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial&lt;BaseParticlesType, BaseMaterialType&gt;</a>* diffusion_reaction_material)</div><div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;            : <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>(body, diffusion_reaction_material)</div><div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;        {</div><div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;            diffusion_reaction_material-&gt;<a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#aab5473ccc3ee73b04028b239cd18614c">assignDiffusionReactionParticles</a>(<span class="keyword">this</span>);</div><div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;            number_of_species_      = diffusion_reaction_material-&gt;<a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#afa18fb6a34828623808f9496176e20a0">getNumberOfSpecies</a>();</div><div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;            species_indexes_map_    = diffusion_reaction_material-&gt;<a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#a32436a338edbc5a36c4e062b612db954">getSpeciesIndexMap</a>();</div><div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i &lt; this-&gt;base_particle_data_.size(); ++i)</div><div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;            {</div><div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;                diffusion_reaction_data_.push_back(<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>(number_of_species_));</div><div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;            }</div><div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;        };</div><div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#af4379007bb1811256664df04c72b9944">   93</a></span>&#160;        <span class="keyword">virtual</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#af4379007bb1811256664df04c72b9944">~DiffusionReactionParticles</a>() {};</div><div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;</div><div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a534d8183f43dc740aca5f76d0b992dec">   96</a></span>&#160;        <a class="code" href="classmap_3_01string_00_01size__t_01_4.html">map&lt;string, size_t&gt;</a> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a534d8183f43dc740aca5f76d0b992dec">getSpeciesIndexMap</a>() { <span class="keywordflow">return</span>  species_indexes_map_; };</div><div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a09bf0b07174be0b619530627f5774c4c">   98</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a09bf0b07174be0b619530627f5774c4c">AddABufferParticle</a>()<span class="keyword"> override </span>{</div><div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;            BaseParticlesType::AddABufferParticle();</div><div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;            diffusion_reaction_data_.push_back(<a class="code" href="class_s_p_h_1_1_diffusion_reaction_data.html">DiffusionReactionData</a>(number_of_species_));</div><div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;        };</div><div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a9a48badab521a63e762f1e2f1c948bab">  103</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a9a48badab521a63e762f1e2f1c948bab">CopyFromAnotherParticle</a>(<span class="keywordtype">size_t</span> this_particle_index,</div><div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;            <span class="keywordtype">size_t</span> another_particle_index)<span class="keyword"> override </span></div><div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;            BaseParticlesType::CopyFromAnotherParticle(this_particle_index, another_particle_index);</div><div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;            diffusion_reaction_data_[this_particle_index] = diffusion_reaction_data_[another_particle_index];</div><div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;        };</div><div class="line"><a name="l00110"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a348cd377a9c4a1a3cfb2173fb96ccf51">  110</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a348cd377a9c4a1a3cfb2173fb96ccf51">swapParticles</a>(<span class="keywordtype">size_t</span> this_particle_index, <span class="keywordtype">size_t</span> that_particle_index)<span class="keyword"> override </span>{</div><div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;            BaseParticlesType::swapParticles(this_particle_index, that_particle_index);</div><div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;            std::swap(diffusion_reaction_data_[this_particle_index], diffusion_reaction_data_[that_particle_index]);</div><div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;        };</div><div class="line"><a name="l00115"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a0543c0e1e0dbcf4d4e03497903351491">  115</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a0543c0e1e0dbcf4d4e03497903351491">WriteParticlesToVtuFile</a>(ofstream&amp; output_file)<span class="keyword"> override </span>{</div><div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;            BaseParticlesType::WriteParticlesToVtuFile(output_file);</div><div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;</div><div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;            map&lt;string, size_t&gt;::iterator itr;</div><div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;            <span class="keywordtype">size_t</span> number_of_particles = this-&gt;body_-&gt;number_of_particles_;</div><div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;            <span class="keywordflow">for</span> (itr = species_indexes_map_.begin(); itr != species_indexes_map_.end(); ++itr) {</div><div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;                output_file &lt;&lt; <span class="stringliteral">&quot;    &lt;DataArray Name=\&quot; &quot;</span>&lt;&lt; itr-&gt;first &lt;&lt;<span class="stringliteral">&quot; \&quot; type=\&quot;Float32\&quot; Format=\&quot;ascii\&quot;&gt;\n&quot;</span>;</div><div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;                output_file &lt;&lt; <span class="stringliteral">&quot;    &quot;</span>;</div><div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;                <span class="keywordtype">size_t</span> k = itr-&gt;second;</div><div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;                <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i != number_of_particles; ++i) {</div><div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;                    output_file &lt;&lt; diffusion_reaction_data_[i].species_n_[k] &lt;&lt; <span class="stringliteral">&quot; &quot;</span>;</div><div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;                }</div><div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;                output_file &lt;&lt; std::endl;</div><div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;                output_file &lt;&lt; <span class="stringliteral">&quot;    &lt;/DataArray&gt;\n&quot;</span>;</div><div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;            }</div><div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;        };</div><div class="line"><a name="l00132"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a7f74782da8540d0a350211f7b53beebd">  132</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a7f74782da8540d0a350211f7b53beebd">WriteParticlesToPltFile</a>(ofstream&amp; output_file)<span class="keyword"> override</span></div><div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;            <span class="comment">//BaseParticlesType::WriteParticlesToPltFile(output_file);</span></div><div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;            <span class="keywordtype">size_t</span> number_of_particles = this-&gt;body_-&gt;number_of_particles_;</div><div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;            map&lt;string, size_t&gt;::iterator itr;</div><div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;            </div><div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;            <span class="keywordflow">if</span>(Vecd(0).size()==2)</div><div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;            {</div><div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;                output_file &lt;&lt; <span class="stringliteral">&quot; VARIABLES = \&quot; x \&quot;, \&quot;y\&quot;, \&quot;ID \&quot; &quot;</span> &lt;&lt; <span class="stringliteral">&quot; &quot;</span>;</div><div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;            }</div><div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;            <span class="keywordflow">if</span>(Vecd(0).size()==3)</div><div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;            {</div><div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;                output_file &lt;&lt; <span class="stringliteral">&quot; VARIABLES = \&quot; x \&quot;, \&quot;y\&quot; , \&quot;z\&quot;, \&quot; ID \&quot; &quot;</span> &lt;&lt; <span class="stringliteral">&quot; &quot;</span>;</div><div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;            }</div><div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;</div><div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;            <span class="keywordflow">for</span> (itr = species_indexes_map_.begin(); itr != species_indexes_map_.end(); ++itr) </div><div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;            {</div><div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;                output_file &lt;&lt; <span class="stringliteral">&quot;,&quot;</span>&lt;&lt; <span class="stringliteral">&quot;\&quot;&quot;</span> &lt;&lt; itr-&gt;first &lt;&lt; <span class="stringliteral">&quot; \&quot; &quot;</span> &lt;&lt; <span class="stringliteral">&quot;&quot;</span>;</div><div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;            }</div><div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;            output_file &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div><div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;</div><div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i != number_of_particles; ++i)</div><div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;            {</div><div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;                <span class="keywordflow">for</span>(<span class="keywordtype">int</span> j = 0; j != Vecd(0).size(); ++j)</div><div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;                {</div><div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;                    output_file &lt;&lt; this-&gt;body_-&gt;base_particles_-&gt;base_particle_data_[i].pos_n_[j] &lt;&lt; <span class="stringliteral">&quot;  &quot;</span>;</div><div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;                }</div><div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;</div><div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;                output_file &lt;&lt; i &lt;&lt; <span class="stringliteral">&quot; &quot;</span>;</div><div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;</div><div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;                <span class="keywordflow">for</span> (itr = species_indexes_map_.begin(); itr != species_indexes_map_.end(); ++itr) </div><div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;                {</div><div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;                    <span class="keywordtype">size_t</span> k = itr-&gt;second;</div><div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;                    output_file &lt;&lt; diffusion_reaction_data_[i].species_n_[k] &lt;&lt; <span class="stringliteral">&quot; &quot;</span>;</div><div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;                }</div><div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;</div><div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;                output_file &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div><div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;            }</div><div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;        };</div><div class="line"><a name="l00172"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a82147e897b82a8135a428df7e8f92c9e">  172</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a82147e897b82a8135a428df7e8f92c9e">WriteParticlesToXmlFile</a>(std::string&amp; filefullpath)<span class="keyword"> override</span>{};</div><div class="line"><a name="l00174"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a96f28c3dd7d94848990362ed378104d7">  174</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a96f28c3dd7d94848990362ed378104d7">WriteParticlesToXmlForRestart</a>(std::string&amp; filefullpath)<span class="keyword"> override </span>{};</div><div class="line"><a name="l00176"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a629b06a5fecda43e3aa5438ab0fbc35a">  176</a></span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a629b06a5fecda43e3aa5438ab0fbc35a">ReadParticleFromXmlForRestart</a>(std::string&amp; filefullpath)<span class="keyword"> override </span>{};</div><div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;        <span class="keyword">virtual</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;</a>* </div><div class="line"><a name="l00179"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#abcbf8afc296e24b934741e33a312fabc">  179</a></span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#abcbf8afc296e24b934741e33a312fabc">PointToThisObject</a>()<span class="keyword"> override </span>{ <span class="keywordflow">return</span> <span class="keyword">this</span>; };</div><div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;    };</div><div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;</div><div class="line"><a name="l00186"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_electro_physiology_particles.html">  186</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_electro_physiology_particles.html">ElectroPhysiologyParticles</a> </div><div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles</a>&lt;SolidParticles, Solid&gt;</div><div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;    {</div><div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;        <a class="code" href="class_s_p_h_1_1_electro_physiology_particles.html">ElectroPhysiologyParticles</a>(<a class="code" href="class_s_p_h_1_1_s_p_h_body.html">SPHBody</a>* body, </div><div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial&lt;SolidParticles, Solid&gt;</a>* diffusion_reaction_material);</div><div class="line"><a name="l00194"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_electro_physiology_particles.html#a9da18e182f1f900b80144b874d0a4b93">  194</a></span>&#160;        <span class="keyword">virtual</span> <a class="code" href="class_s_p_h_1_1_electro_physiology_particles.html#a9da18e182f1f900b80144b874d0a4b93">~ElectroPhysiologyParticles</a>() {};</div><div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;</div><div class="line"><a name="l00197"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_electro_physiology_particles.html#a4569b900d957e5bcbf5216b6e1c70f00">  197</a></span>&#160;        <span class="keyword">virtual</span> <a class="code" href="class_s_p_h_1_1_electro_physiology_particles.html">ElectroPhysiologyParticles</a>* <a class="code" href="class_s_p_h_1_1_electro_physiology_particles.html#a4569b900d957e5bcbf5216b6e1c70f00">PointToThisObject</a>()<span class="keyword"> override </span>{ <span class="keywordflow">return</span> <span class="keyword">this</span>; };</div><div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;    };</div><div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;}</div><div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_a9a48badab521a63e762f1e2f1c948bab"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#a9a48badab521a63e762f1e2f1c948bab">SPH::DiffusionReactionParticles::CopyFromAnotherParticle</a></div><div class="ttdeci">virtual void CopyFromAnotherParticle(size_t this_particle_index, size_t another_particle_index) override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:103</div></div>
<div class="ttc" id="class_s_p_h_1_1_electro_physiology_particles_html_a9da18e182f1f900b80144b874d0a4b93"><div class="ttname"><a href="class_s_p_h_1_1_electro_physiology_particles.html#a9da18e182f1f900b80144b874d0a4b93">SPH::ElectroPhysiologyParticles::~ElectroPhysiologyParticles</a></div><div class="ttdeci">virtual ~ElectroPhysiologyParticles()</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:194</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_af4fd7b9302042ace3975690235e3cf25"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#af4fd7b9302042ace3975690235e3cf25">SPH::DiffusionReactionParticles::number_of_species_</a></div><div class="ttdeci">size_t number_of_species_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:73</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_af4379007bb1811256664df04c72b9944"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#af4379007bb1811256664df04c72b9944">SPH::DiffusionReactionParticles::~DiffusionReactionParticles</a></div><div class="ttdeci">virtual ~DiffusionReactionParticles()</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:93</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_a0543c0e1e0dbcf4d4e03497903351491"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#a0543c0e1e0dbcf4d4e03497903351491">SPH::DiffusionReactionParticles::WriteParticlesToVtuFile</a></div><div class="ttdeci">virtual void WriteParticlesToVtuFile(ofstream &amp;output_file) override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:115</div></div>
<div class="ttc" id="namespacestd_html"><div class="ttname"><a href="namespacestd.html">std</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_ab0a715f35dc6105562f81bac0eb2852b"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#ab0a715f35dc6105562f81bac0eb2852b">SPH::DiffusionReactionParticles::DiffusionReactionParticles</a></div><div class="ttdeci">DiffusionReactionParticles(SPHBody *body, DiffusionReactionMaterial&lt; BaseParticlesType, BaseMaterialType &gt; *diffusion_reaction_material)</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:80</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html">SPH::DiffusionReactionMaterial</a></div><div class="ttdoc">Complex material for diffusion or/and reactions. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:263</div></div>
<div class="ttc" id="xml__engine_8h_html"><div class="ttname"><a href="xml__engine_8h.html">xml_engine.h</a></div><div class="ttdoc">XML class for xml input and output, this is GUI of simbody xml parser. </div></div>
<div class="ttc" id="class_s_p_h_1_1_electro_physiology_particles_html"><div class="ttname"><a href="class_s_p_h_1_1_electro_physiology_particles.html">SPH::ElectroPhysiologyParticles</a></div><div class="ttdoc">A group of particles with electrophysiology particle data. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:186</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_a09bf0b07174be0b619530627f5774c4c"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#a09bf0b07174be0b619530627f5774c4c">SPH::DiffusionReactionParticles::AddABufferParticle</a></div><div class="ttdeci">virtual void AddABufferParticle() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:98</div></div>
<div class="ttc" id="base__body_8h_html"><div class="ttname"><a href="base__body_8h.html">base_body.h</a></div><div class="ttdoc">This is the base classes of SPH bodies. The real body is for that with cell linked list and the ficti...</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_data_html_a9c9c5fa76e83b20f66c7eb961dea9b76"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_data.html#a9c9c5fa76e83b20f66c7eb961dea9b76">SPH::DiffusionReactionData::dspecies_dt_</a></div><div class="ttdeci">StdVec&lt; Real &gt; dspecies_dt_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:61</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_particles_type_html"><div class="ttname"><a href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_abcbf8afc296e24b934741e33a312fabc"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#abcbf8afc296e24b934741e33a312fabc">SPH::DiffusionReactionParticles::PointToThisObject</a></div><div class="ttdeci">virtual DiffusionReactionParticles&lt; BaseParticlesType, BaseMaterialType &gt; * PointToThisObject() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:179</div></div>
<div class="ttc" id="classmap_3_01string_00_01size__t_01_4_html"><div class="ttname"><a href="classmap_3_01string_00_01size__t_01_4.html">map&lt; string, size_t &gt;</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_data_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_data.html">SPH::DiffusionReactionData</a></div><div class="ttdoc">Particles data for general diffusion/reaction problems. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:49</div></div>
<div class="ttc" id="base__material_8h_html"><div class="ttname"><a href="base__material_8h.html">base_material.h</a></div><div class="ttdoc">This is the base classes of all materials. A function in a derived material class returns a value wit...</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_a32436a338edbc5a36c4e062b612db954"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a32436a338edbc5a36c4e062b612db954">SPH::DiffusionReactionMaterial::getSpeciesIndexMap</a></div><div class="ttdeci">map&lt; string, size_t &gt; getSpeciesIndexMap()</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:314</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_aab5473ccc3ee73b04028b239cd18614c"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#aab5473ccc3ee73b04028b239cd18614c">SPH::DiffusionReactionMaterial::assignDiffusionReactionParticles</a></div><div class="ttdeci">void assignDiffusionReactionParticles(DiffusionReactionParticles&lt; BaseParticlesType, BaseMaterialType &gt; *diffusion_reaction_particles)</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:316</div></div>
<div class="ttc" id="class_s_p_h_1_1_electro_physiology_particles_html_a4569b900d957e5bcbf5216b6e1c70f00"><div class="ttname"><a href="class_s_p_h_1_1_electro_physiology_particles.html#a4569b900d957e5bcbf5216b6e1c70f00">SPH::ElectroPhysiologyParticles::PointToThisObject</a></div><div class="ttdeci">virtual ElectroPhysiologyParticles * PointToThisObject() override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:197</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_material_html_afa18fb6a34828623808f9496176e20a0"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#afa18fb6a34828623808f9496176e20a0">SPH::DiffusionReactionMaterial::getNumberOfSpecies</a></div><div class="ttdeci">size_t getNumberOfSpecies()</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:308</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_a629b06a5fecda43e3aa5438ab0fbc35a"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#a629b06a5fecda43e3aa5438ab0fbc35a">SPH::DiffusionReactionParticles::ReadParticleFromXmlForRestart</a></div><div class="ttdeci">virtual void ReadParticleFromXmlForRestart(std::string &amp;filefullpath) override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:176</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_a348cd377a9c4a1a3cfb2173fb96ccf51"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#a348cd377a9c4a1a3cfb2173fb96ccf51">SPH::DiffusionReactionParticles::swapParticles</a></div><div class="ttdeci">virtual void swapParticles(size_t this_particle_index, size_t that_particle_index) override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:110</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_ace9886026ada5948e27c14a0ce827b2f"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#ace9886026ada5948e27c14a0ce827b2f">SPH::DiffusionReactionParticles::diffusion_reaction_data_</a></div><div class="ttdeci">StdLargeVec&lt; DiffusionReactionData &gt; diffusion_reaction_data_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:77</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_data_html_a225749466f115c22bae74deb18140ce7"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_data.html#a225749466f115c22bae74deb18140ce7">SPH::DiffusionReactionData::species_s_</a></div><div class="ttdeci">StdVec&lt; Real &gt; species_s_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:59</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_a96f28c3dd7d94848990362ed378104d7"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#a96f28c3dd7d94848990362ed378104d7">SPH::DiffusionReactionParticles::WriteParticlesToXmlForRestart</a></div><div class="ttdeci">virtual void WriteParticlesToXmlForRestart(std::string &amp;filefullpath) override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:174</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_a82147e897b82a8135a428df7e8f92c9e"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#a82147e897b82a8135a428df7e8f92c9e">SPH::DiffusionReactionParticles::WriteParticlesToXmlFile</a></div><div class="ttdeci">virtual void WriteParticlesToXmlFile(std::string &amp;filefullpath) override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:172</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html">SPH::DiffusionReactionParticles</a></div><div class="ttdoc">A group of particles with diffusion or/and reactions particle data. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:45</div></div>
<div class="ttc" id="class_std_vec_3_01_real_01_4_html"><div class="ttname"><a href="class_std_vec_3_01_real_01_4.html">StdVec&lt; Real &gt;</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_s_p_h_body_html"><div class="ttname"><a href="class_s_p_h_1_1_s_p_h_body.html">SPH::SPHBody</a></div><div class="ttdoc">SPHBody is a base body with basic data and functions. Its derived class can be a real fluid body...</div><div class="ttdef"><b>Definition:</b> base_body.h:73</div></div>
<div class="ttc" id="solid__particles_8h_html"><div class="ttname"><a href="solid__particles_8h.html">solid_particles.h</a></div><div class="ttdoc">This is the derived class of base particle. </div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_a7f74782da8540d0a350211f7b53beebd"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#a7f74782da8540d0a350211f7b53beebd">SPH::DiffusionReactionParticles::WriteParticlesToPltFile</a></div><div class="ttdeci">virtual void WriteParticlesToPltFile(ofstream &amp;output_file) override</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:132</div></div>
<div class="ttc" id="namespace_s_p_h_html"><div class="ttname"><a href="namespace_s_p_h.html">SPH</a></div><div class="ttdef"><b>Definition:</b> base_body_supplementary.cpp:11</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_particles_html_a534d8183f43dc740aca5f76d0b992dec"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#a534d8183f43dc740aca5f76d0b992dec">SPH::DiffusionReactionParticles::getSpeciesIndexMap</a></div><div class="ttdeci">map&lt; string, size_t &gt; getSpeciesIndexMap()</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:96</div></div>
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